[Debian-med-packaging] Bug#844900: sra-sdk: FTBFS: libncbi-vdb.so: undefined reference to `mbedtls_x509_crt_parse_file'

[Adrian Bunk]

Control: reassign -1 libncbi-vdb2
Control: affects -1 src:sra-sdk
Control: retitle -1 libncbi-vdb.so.2 is not linked with all libraries

On Sat, Nov 19, 2016 at 07:50:15AM +0100, Lucas Nussbaum wrote:
>...
> > /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_entropy_free'
> > /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_read'
> > /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_x509_crt_free'
> > /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_entropy_func'
> > /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_conf_rng'
> > /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_ssl_write'
> > /usr/lib/x86_64-linux-gnu/libncbi-vdb.so: undefined reference to `mbedtls_x509_crt_verify_info'
> > collect2: error: ld returned 1 exit status
>...

The actual bug is in libncbi-vdb2,
relevant part from the ncbi-vdb build log[1]:

...
dpkg-shlibdeps: warning: symbol mbedtls_ctr_drbg_init used by debian/libncbi-vdb2/usr/lib/i386-linux-gnu/libncbi-vdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ssl_set_bio used by debian/libncbi-vdb2/usr/lib/i386-linux-gnu/libncbi-vdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ssl_conf_rng used by debian/libncbi-vdb2/usr/lib/i386-linux-gnu/libncbi-vdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ssl_get_verify_result used by debian/libncbi-vdb2/usr/lib/i386-linux-gnu/libncbi-vdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_strerror used by debian/libncbi-vdb2/usr/lib/i386-linux-gnu/libncbi-vdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_x509_crt_free used by debian/libncbi-vdb2/usr/lib/i386-linux-gnu/libncbi-vdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ctr_drbg_seed used by debian/libncbi-vdb2/usr/lib/i386-linux-gnu/libncbi-vdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ssl_config_init used by debian/libncbi-vdb2/usr/lib/i386-linux-gnu/libncbi-vdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ssl_free used by debian/libncbi-vdb2/usr/lib/i386-linux-gnu/libncbi-vdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_entropy_free used by debian/libncbi-vdb2/usr/lib/i386-linux-gnu/libncbi-vdb.so.2.8.0 found in none of the libraries
...
dpkg-shlibdeps: warning: symbol mbedtls_ssl_get_verify_result used by debian/libncbi-wvdb2/usr/lib/i386-linux-gnu/libncbi-wvdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ssl_set_bio used by debian/libncbi-wvdb2/usr/lib/i386-linux-gnu/libncbi-wvdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ssl_init used by debian/libncbi-wvdb2/usr/lib/i386-linux-gnu/libncbi-wvdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ssl_close_notify used by debian/libncbi-wvdb2/usr/lib/i386-linux-gnu/libncbi-wvdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ctr_drbg_init used by debian/libncbi-wvdb2/usr/lib/i386-linux-gnu/libncbi-wvdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ssl_handshake used by debian/libncbi-wvdb2/usr/lib/i386-linux-gnu/libncbi-wvdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ssl_write used by debian/libncbi-wvdb2/usr/lib/i386-linux-gnu/libncbi-wvdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ctr_drbg_seed used by debian/libncbi-wvdb2/usr/lib/i386-linux-gnu/libncbi-wvdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_ssl_conf_rng used by debian/libncbi-wvdb2/usr/lib/i386-linux-gnu/libncbi-wvdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mbedtls_x509_crt_verify_info used by debian/libncbi-wvdb2/usr/lib/i386-linux-gnu/libncbi-wvdb.so.2.8.0 found in none of the libraries
dpkg-shlibdeps: warning: 19 other similar warnings have been skipped (use -v to see them all)
...

cu
Adrian

[1] https://buildd.debian.org/status/fetch.php?pkg=ncbi-vdb&arch=i386&ver=2.8.0+dfsg-1&stamp=1478253717

-- 

       "Is there not promise of rain?" Ling Tan asked suddenly out
        of the darkness. There had been need of rain for many days.
       "Only a promise," Lao Er said.
                                       Pearl S. Buck - Dragon Seed